It seems that motorbox needs to be propped up slightly and you need tools from both sides. Is it easier to remove hardware from motorbox or floor side of hinge?

I agree with Mike- it is easy to handle if the floor section remains attached to the cover and it also avoids damaging the honeycomb material or losing the nuts/washers. You'll probably find it easiest to release the shocks, tilt the cover back (DON'T let it fall back), lift gently on the front edge of the floor section and pull forward as you lift, so it clears the rear of the engine/transmission. Once the floor clears the bottom of the seat, you can lift it out or lay it on the rear pad, upside down. You can buy moving blankets from U-Haul or Harbor Freight to avoid damage/dirt on the vinyl padding.